segunda-feira, outubro 31, 2011

Michelson and Morley showed that an interference pattern is reference-frame independent. However, the distance between a particle's production and detection site is reference-frame dependent due to Lorentz contraction and detector movement. For the OPERA experiment detector movement in the satellite reference frame leads to corrections which can account for most of the $\pm 60$ ns discrepancy between expected and observed time of flight.

Comments: 4 pages; Version 3: Rephrased large parts of the paper. I try to respond to latest developments on my website

Head injury is a leading cause of morbidity and death in both industrialized and developing countries. It is estimated that brain injuries account for 15% of the burden of fatalities and disabilities, and represent the leading cause of death in young adults. Brain injury may be caused by an impact or a sudden change in the linear and/or angular velocity of the head. However, the woodpecker does not experience any head injury at the high speed of 6–7 m/s with a deceleration of 1000 g when it drums a tree trunk. It is still not known how woodpeckers protect their brain from impact injury. In order to investigate this, two synchronous high-speed video systems were used to observe the pecking process, and the force sensor was used to measure the peck force. The mechanical properties and macro/micro morphological structure in woodpecker's head were investigated using a mechanical testing system and micro-CT scanning. Finite element (FE) models of the woodpecker's head were established to study the dynamic intracranial responses. The result showed that macro/micro morphology of cranial bone and beak can be recognized as a major contributor to non-impact-injuries. This biomechanical analysis makes it possible to visualize events during woodpecker pecking and may inspire new approaches to prevention and treatment of human head injury.

Long-term effects of ovarian stimulation for IVF on the risk of ovarian malignancies are unknown.

METHODS

We identified a nationwide historic cohort of 19 146 women who received IVF treatment in the Netherlands between 1983 and 1995, and a comparison group of 6006 subfertile women not treated with IVF. In 1997–1999, data on reproductive risk factors were obtained from 65% of women and data on subfertility (treatment) were obtained from the medical records. The incidence of ovarian malignancies (including borderline ovarian tumours) through 2007 was assessed through linkage with disease registries. The risk of ovarian malignancies in the IVF group was compared with risks in the general population and the subfertile comparison group.

RESULTS

After a median follow-up of 14.7 years, the risk of borderline ovarian tumours was increased in the IVF group compared with the general population [standardized incidence ratio (SIR) = 1.76; 95% confidence interval (CI) = 1.16–2.56]. The overall SIR for invasive ovarian cancer was not significantly elevated, but increased with longer follow-up after first IVF (P= 0.02); the SIR was 3.54 (95% CI = 1.62–6.72) after 15 years. The risks of borderline ovarian tumours and of all ovarian malignancies combined in the IVF group were significantly increased compared with risks in the subfertile comparison group (hazard ratios = 4.23; 95% CI = 1.25–14.33 and 2.14; 95% CI = 1.07–4.25, respectively, adjusted for age, parity and subfertility cause).

CONCLUSIONS

Ovarian stimulation for IVF may increase the risk of ovarian malignancies, especially borderline ovarian tumours. More large cohort studies are needed to confirm these findings and to examine the effect of IVF treatment characteristics.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

First paragraph: "The twentieth century was the bloodiest in history." This frequently asserted claim is popular among the romantic, the religious, the nostalgic and the cynical. They use it to impugn a range of ideas that flourished in that century, including science, reason, secularism, Darwinism and the ideal of progress. But this historical factoid is rarely backed up by numbers, and it is almost certainly an illusion. We are prone to think that modern life is more violent because historical records from recent eras are more complete, and because the human mind overestimates the frequency of vivid, memorable events. We also care more about violence today. Ancient histories are filled with glorious conquests that today would be classified as genocide, and the leaders known to history as So-and-So the Great would today be prosecuted as war criminals.

Around 60,000 historical scientific papers are accessible via a fully searchable online archive, with papers published more than 70 years ago now becoming freely available.

The Royal Society is the world’s oldest scientific publisher, with the first edition of Philosophical Transactions of the Royal Society appearing in 1665. Henry Oldenburg – Secretary of the Royal Society and first Editor of the publication – ensured that it was “licensed by the council of the society, being first reviewed by some of the members of the same”, thus making it the first ever peer-reviewed journal.

Philosophical Transactions had to overcome early setbacks including plague, the Great Fire of London and even the imprisonment of Oldenburg, but against the odds the publication survived to the present day. Its foundation would eventually be recognised as one of the most pivotal moments of the scientific revolution.

Professor Uta Frith FRS, Chair of the Royal Society library committee, said: “I’m delighted that the Royal Society is continuing to increase access to its wonderful resources by opening up its publishing archives. The release of these papers opens a fascinating window on the history of scientific progress over the last few centuries and will be of interest to anybody who wants to understand how science has evolved since the days of the Royal Society’s foundation.”

Henry Oldenburg writes in his introduction to the first edition: “...it is therefore thought fit to employ the Press, as the most proper way to gratify those, whose...delight in the advancement of Learning and profitable Discoveries, doth entitle them to the knowledge of what this Kingdom, or other parts of the World, do, from time to time, afford...”, going on to state that potential contributors are: “...invited and encouraged to search, try, and find out new things, impart their knowledge to one another, and contribute what they can to the Grand design of improving natural knowledge, and perfecting all Philosophical Arts, and Sciences.”

Thomas Huxley FRS wrote in 1870: “If all the books in the world, except the Philosophical Transactions, were to be destroyed, it is safe to say that the foundations of physical science would remain unshaken, and that the vast intellectual progress of the last two centuries would be largely, though incompletely, recorded.”

The move is being made as part of the Royal Society’s ongoing commitment to open access in scientific publishing. Opening of the archive is being timed to coincide with Open Access Week, and also comes soon after the Royal Society announced its first ever fully open access journal, Open Biology.

eDepartment of Ecology and Evolution, University of Chicago, Chicago, IL 60637; and

fBiodiversity Research Center, Academia Sinica, Taipei 115, Taiwan

Contributed by Wen-Hsiung Li, September 26, 2011 (sent for review May 29, 2011)

Abstract

Since the sensational discovery of a living coelacanth off the east coast of South Africa, the geographic distribution of viable coelacanth populations has been a subject of debate. In the past, the coelacanths off the African mainland were thought to be strays from the Comoros because most coelacanths captured were caught in the waters surrounding the Comoros archipelagos. However, in recent years, a large number of coelacanths were captured off the coast of Tanzania, including nine living specimens observed in a remotely operated vehicles survey. Thus, it is possible that there is a reproducing population inhabiting waters off the Tanzania coast. We have sequenced the complete mitochondrial genomes of 21 Tanzanian and 2 Comoran coelacanths and analyzed these sequences together with two additional full mitochondrial genomes and 47 d-loop sequences from the literature. We found that the coelacanth population off the northern Tanzanian coast is genetically differentiated from those of the southern Tanzania coast and the Comoros, whereas no significant genetic differentiation occurs between the latter two localities. The differentiation between the northern and southern Tanzanian coast populations is consistent with the hypothesis that the existence of northward-flowing ocean current along the Tanzanian coast may reduce or prevent gene flow from the northern to the southern population. Finally, we estimated that the population localized to the southern Tanzanian coast and the Comoros diverged from other coelacanths at least 200,000 y ago. These results indicate that the coelacanths off the northern Tanzania coast are not strays but a genetically distinct group. Our study provides important information for the conservation of this threatened “living fossil.”

segunda-feira, outubro 24, 2011

Edited by David M. Hillis, University of Texas at Austin, Austin, TX, and approved March 2, 2011 (received for review November 9, 2010)

Abstract

Phylogenetic trees of present-day species allow investigation of the rate of evolution that led to the present-day diversity. A recent analysis of the mammalian phylogeny challenged the view of explosive mammalian evolution after the Cretaceous–Tertiary (K/T) boundary (65 Mya). However, due to lack of appropriate methods, the diversification (speciation minus extinction) rates in the more recent past of mammalian evolution could not be determined. In this paper, I provide a method that reveals that the tempo of mammalian evolution did not change until ∼33 Mya. This constant period was followed by a peak of diversification rates between 33 and 30 Mya. Thereafter, diversification rates remained high and constant until 8.55 Mya. Diversification rates declined significantly at 8.55 and 3.35 Mya. Investigation of mammalian subgroups (marsupials, placentals, and the six largest placental subgroups) reveals that the diversification rate peak at 33–30 Mya is mainly driven by rodents, cetartiodactyla, and marsupials. The recent diversification rate decrease is significant for all analyzed subgroups but eulipotyphla, cetartiodactyla, and primates. My likelihood approach is not limited to mammalian evolution. It provides a robust framework to infer diversification rate changes and mass extinction events in phylogenies, reconstructed from, e.g., present-day species or virus data. In particular, the method is very robust toward noise and uncertainty in the phylogeny and can account for incomplete taxon sampling.

Querying the past is hard. Speciation and extinction processes are on a scale of thousands to millions of years. Thus, they are most often studied by reconstructing the evolutionary past. This past is reconstructed using phylogenetic methods either on the basis of data from living species or by directly examining the fossil record. Robust methods for inferring the evolutionary past purely on the basis of living species would allow us to understand speciation and extinction processes for the large number of groups without a good fossil record.

Generally, studies using living species infer lower extinction rates than the rates suggested by the fossil record ( 1, 2). A new study in PNAS ( 3) suggests that this mismatch is due to our use of oversimplified models of speciation and extinction.

Fifteen years ago, Nee et al. ( 4) presented the first method to infer speciation and extinction rates on the basis of “reconstructed” phylogenies, i.e., phylogenies inferred on only extant species ( Fig. 1 A and B ). This first likelihood method relied on the idea that lineages in a reconstructed phylogeny accumulate through time with rate λ − μ (where λ is the speciation rate and μ is the extinction rate) and accumulate in the very recent past with rate λ. The change in rate of lineage accumulation from λ − μ to λ, called the “pull-of-the-present” (5), allows us to estimate both λ and μ given only data from living species.

Fig. 1.

( A and B) Complete phylogeny ( A) with associated reconstructed phylogeny ( B), which is obtained by suppressing all extinct lineages. ( C– G)Models for speciation and extinction. Red denotes a fast rate, purple an intermediate rate, and blue a slow rate of speciation. C–E indicate the three models accounting for rate heterogeneity through time and across subclades: ( C) Morlon …

Edited* by Robert E. Ricklefs, University of Missouri, St. Louis, MO, and approved August 1, 2011 (received for review February 14, 2011)

Abstract

Historical patterns of species diversity inferred from phylogenies typically contradict the direct evidence found in the fossil record. According to the fossil record, species frequently go extinct, and many clades experience periods of dramatic diversity loss. However, most analyses of molecular phylogenies fail to identify any periods of declining diversity, and they typically infer low levels of extinction. This striking inconsistency between phylogenies and fossils limits our understanding of macroevolution, and it undermines our confidence in phylogenetic inference. Here, we show that realistic extinction rates and diversity trajectories can be inferred from molecular phylogenies. To make this inference, we derive an analytic expression for the likelihood of a phylogeny that accommodates scenarios of declining diversity, time-variable rates, and incomplete sampling; we show that this likelihood expression reliably detects periods of diversity loss using simulation. We then study the cetaceans (whales, dolphins, and porpoises), a group for which standard phylogenetic inferences are strikingly inconsistent with fossil data. When the cetacean phylogeny is considered as a whole, recently radiating clades, such as the Balaneopteridae, Delphinidae, Phocoenidae, and Ziphiidae, mask the signal of extinctions. However, when isolating these groups, we infer diversity dynamics that are consistent with the fossil record. These results reconcile molecular phylogenies with fossil data, and they suggest that most extant cetaceans arose from four recent radiations, with a few additional species arising from clades that have been in decline over the last ∼10 Myr.

Author contributions: H.M. and J.B.P. designed research; H.M., T.L.P., and J.B.P. performed research; H.M. and T.L.P. contributed new reagents/analytic tools; H.M. analyzed data; and H.M., T.L.P., and J.B.P. wrote the paper.

Bacteria communicate with one another using small chemical molecules that they release into the environment. These molecules travel from cell to cell and the bacteria have receptors on their surfaces that allow them to detect and respond to the build up of the molecules. This process of cell-to-cell communication in bacteria is called “Quorum Sensing” and it allows bacteria to synchronize behavior on a population-wide scale. Bacterial behaviors controlled by quorum sensing are usually ones that are unproductive when undertaken by an individual bacterium acting alone but become effective when undertaken in unison by the group. For example, quorum sensing controls virulence, sporulation, and the exchange of DNA. Thus, quorum sensing is a mechanism that allows bacteria to function as multi-cellular organisms. Current biomedical research is focused on the development of novel anti-bacterial therapies aimed at interfering with quorum sensing. Such therapies could be used to control bacterial pathogenicity.

Bonnie Bassler is a member of the National Academy of Sciences and the American Academy of Arts and Sciences. She is a Howard Hughes Medical Institute Investigator and the Squibb Professor of Molecular Biology at Princeton University. Bassler received a B.S. in Biochemistry from the University of California at Davis, and a Ph.D. in Biochemistry from the Johns Hopkins University. She performed postdoctoral work in Genetics at the Agouron Institute, and she joined the Princeton faculty in 1994. The research in her laboratory focuses on the molecular mechanisms that bacteria use for intercellular communication. This process is called quorum sensing. Bassler’s research is paving the way to the development of novel therapies for combating bacteria by disrupting quorum-sensing-mediated communication. At Princeton, Dr. Bassler teaches both undergraduate and graduate courses. Dr. Bassler directed the Molecular Biology Graduate Program from 2002-2008 and she currently chairs Princeton University’s Council on Science and Technology which has revamped the science curriculum for humanists. Bassler is a passionate advocate for diversity in the sciences and she is actively involved in and committed to educating lay people in science. Dr. Bassler was awarded a MacArthur Foundation Fellowship in 2002. She was elected to the American Academy of Microbiology in 2002 and made a fellow of the American Association for the Advancement of Science in 2004. She was given the 2003 Theobald Smith Society Waksman Award and she is the 2006 recipient of the American Society for Microbiology’s Eli Lilly Investigator Award for fundamental contributions to microbiological research. In 2008, Bassler was given Princeton University’s President’s Award for Distinguished Teaching. She is the 2009 recipient of the Wiley Prize in Biomedical Science for her paradigm-changing scientific research. She is the 2011 recipient of the National Academies’ Richard Lounsbery Award. Bassler is the President of the American Society for Microbiology, an editor for Molecular Microbiology, mBio, and Chief Editor of Annual Reviews of Genetics. She is an associate editor for Cell, Proceedings of the National Academy of Sciences, Journal of Bacteriology, and other journals. Among other duties, she serves on the National Academies Board on Life Sciences, the Howard Hughes Medical Institute Science Education Committee, and Discovery Communications’ Science Channel Scientific Advisory Board. She sits on the Scientific Advisory Boards of Cubist Pharmaceuticals and Pfizer Global Research. She serves on oversight, grant, fellowship, and award panels for the National Academies of Sciences, National Institutes of Health, National Science Foundation, American Society for Microbiology, American Academy of Microbiology, Keck Foundation, Burroughs Wellcome Trust, Jane Coffin Childs Fund, MIT Whitehead Institute, and the Max Planck Society.

"When we consider the remote past, before the origin of the actual species Homo sapiens, we are faced with a fragmentary and disconnected fossil record. Despite the excited and optimistic claims that have been made by some paleontologists, no fossil hominid species can be established as our direct ancestor".

Excerpt: “Definition of the genus Homo is almost as fraught as the definition of Homo sapiens. We look at the evidence for “early Homo,” finding little morphological basis for extending our genus to any of the 2.5–1.6-myr-old fossil forms assigned to “early Homo” or Homo habilis/rudolfensis.”

“Something extraordinary, if totally fortuitous, happened with the birth of our species….Homo sapiens is as distinctive an entity as exists on the face of the Earth, and should be dignified as such instead of being adulterated with every reasonably large-brained hominid fossil that happened to come along.”

Anthropologist Ian Tattersall – curator at the American Museum of Natural History

“The australopithecines (Lucy) known over the last several decades from Olduvai and Sterkfontein, Kromdraai and Makapansgat, are now irrevocably removed from a place in a group any closer to humans than to African apes and certainly from any place in a direct human lineage.”

Charles Oxnard, former professor of anatomy at the University of Southern California Medical School, who subjected australopithecine fossils to extensive computer analysis;

The Mandibular ramus morphology (lower jaw bone) on a recently discovered specimen of Australopithecus afarensis closely matches that of gorillas. This finding was unexpected given that chimpanzees are the closest living relatives of humans.,,,its absence in modern humans cast doubt on the role of Au. afarensis as a modern human ancestor.

“If pressed about man’s ancestry, I would have to unequivocally say that all we have is a huge question mark. To date, there has been nothing found to truthfully purport as a transitional species to man, including Lucy, since 1470 was as old and probably older. If further pressed, I would have to state that there is more evidence to suggest an abrupt arrival of man rather than a gradual process of evolving”.

Excerpt: the current criteria for identifying species of Homo are difficult, if not impossible, to operate using paleoanthropological evidence. We discuss alternative, verifiable, criteria, and show that when these new criteria are applied to Homo, two species, Homo habilis and Homo rudolfensis, fail to meet them.

Excerpt: Some scientists have proposed moving this species (habilis) out of Homo and into Australopithecus (ape) due to the morphology of its skeleton being more adapted to living on trees rather than to moving on two legs like H. sapiens.

Who Was Homo habilis—And Was It Really Homo? – Ann Gibbons – June 2011

Abstract: In the past decade, Homo habilis’s status as the first member of our genus has been undermined. Newer analytical methods suggested that H. habilis matured and moved less like a human and more like an australopithecine, such as the famous partial skeleton of Lucy. Now, a report in press in the Journal of Human Evolution finds that H. habilis’s dietary range was also more like Lucy’s than that of H. erectus, which many consider the first fully human species to walk the earth. That suggests the handyman had yet to make the key adaptations associated with our genus, such as the ability to exploit a variety of foods in many environments, the authors say.

Excerpt: The old theory was that the first and oldest species in our family tree, Homo habilis, evolved into Homo erectus, which then became us, Homo sapiens. But those two earlier species lived side-by-side about 1.5 million years ago in parts of Kenya for at least half a million years,,, The two species lived near each other, but probably didn’t interact with each other, each having their own “ecological niche,” Spoor said. Homo habilis was likely more vegetarian and Homo erectus ate some meat, he said. Like chimps and apes, “they’d just avoid each other, they don’t feel comfortable in each other’s company,” he said.

Excerpt: “It is practically impossible to determine which “family tree” (for human evolution) one should accept. Richard Leakey (of the famed fossil hunting family from Africa) has proposed one. His late mother, Mary Leakey, proposed another. Donald Johanson, former president of the Institute of Human Origins in Berkeley, California, has proposed yet another. And as late as 2001, Meave Leakey (Richard’s wife) has proposed still another...”

“The earliest fossils of Homo, Homo rudolfensis and Homo erectus, are separated from Australopithecus (Lucy) by a large, unbridged gap. How can we explain this seeming saltation? Not having any fossils that can serve as missing links, we have to fall back on the time-honored method of historical science, the construction of a historical narrative.”Misrepresentations of the Evidence for Human Evolutionary Originshttp://www.evolutionnews.org/2......html#more

Darwin’s mistake: Explaining the discontinuity between human and nonhuman minds

Excerpt: There is a profound functional discontinuity between human and nonhuman minds. We argue that this discontinuity pervades nearly every domain of cognition and runs much deeper than even the spectacular scaffolding provided by language or culture can explain. We hypothesize that the cognitive discontinuity between human and nonhuman animals is largely due to the degree to which human and nonhuman minds are able to approximate the higher-order, systematic, relational capabilities of a physical symbol system.

Excerpt: “Researchers have found some of the building blocks of human cognition in other species. But these building blocks make up only the cement footprint of the skyscraper that is the human mind”,,,

Earliest humans not so different from us, research suggests – February 2011

Excerpt: Shea argues that comparing the behavior of our most ancient ancestors to Upper Paleolithic Europeans holistically and ranking them in terms of their “behavioral modernity” is a waste of time. There are no such things as modern humans, Shea argues, just Homo sapiens populations with a wide range of behavioral variability.

Excerpt: the International Chimpanzee Chromosome 22 Consortium reports that 83% of chimpanzee chromosome 22 proteins are different from their human counterparts,,, The results reported this week showed that “83% of the genes have changed between the human and the chimpanzee—only 17% are identical—so that means that the impression that comes from the 1.2% [sequence] difference is [misleading]. In the case of protein structures, it has a big effect,” Sakaki said.

Chimp chromosome creates puzzles – 2004

Excerpt: However, the researchers were in for a surprise. Because chimps and humans appear broadly similar, some have assumed that most of the differences would occur in the large regions of DNA that do not appear to have any obvious function. But that was not the case. The researchers report in ‘Nature’ that many of the differences were within genes, the regions of DNA that code for proteins. 83% of the 231 genes compared had differences that affected the amino acid sequence of the protein they encoded. And 20% showed “significant structural changes”. In addition, there were nearly 68,000 regions that were either extra or missing between the two sequences, accounting for around 5% of the chromosome.,,, “we have seen a much higher percentage of change than people speculated.” The researchers also carried out some experiments to look at when and how strongly the genes are switched on. 20% of the genes showed significant differences in their pattern of activity.

Excerpt: For about 23% of our genome, we share no immediate genetic ancestry with our closest living relative, the chimpanzee. This encompasses genes and exons to the same extent as intergenic regions. We conclude that about 1/3 of our genes started to evolve as human-specific lineages before the differentiation of human, chimps, and gorillas took place. (of note; 1/3 of our genes is equal to about 7000 genes that we do not share with chimpanzees)